I only have access to jopr right now. So the only way i can get the recovery alerts working is if I create them at the alert definition level? what if I create an alert template for availability going down but then create seperate alert defintions under each jboss application server, will that work?

If you have administrator access to Jopr, then log in as the administrator and go to /admin/test/sql.jsp - it gives you full SQL access to the backing data store, which will allow you to run the query mentioned in RHQ-2150 if you want to use the workaround for alert templates.

That's correct. The SQL should "fix" the broken recovery alerts, which in your case are the resource-level alert definition that would get created when #2 and #4 are applied to all JBAS instances in your inventory.